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MUD transcript:  23-03-00

Molecular Forces

Course room(s): PPS 

15:58:29  CharafB connects.

ClareS       PPS          HTTP     5m 45s   5m 27s
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15:58:44  ClareS says "Hi"
15:58:52  CharafB says (to ClareS) "Hello, Clare"
15:59:05  ClareS says "I'd like to wait a couple of minutes before starting"
15:59:22  ClareS says "(I don't think it's even quite 16:00 yet)"
15:59:57  CharafB says "no problem... :)"
16:02:36  ClareS says "is your connection OK? Mine is rather slow"
16:02:37  ClareS says "(I don't think it's even quite 16:00 yet)"
16:04:42  SpyrosS connects.
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16:04:42  CharafB says "mine seems ok... I hope!"
16:05:14  SpyrosS says "Hi everyone"
16:05:28  CharafB says (to Spir) "Hi"
16:05:31  ClareS says "Hi"
16:06:12  ClareS says "I guess we might as well start now... I am sure latecomers will join in OK"
16:06:26  ClareS says "how have you found the Molecular Forces section?"
16:07:43  CharafB says "It was really interesting but seemed very theoretical to me"
16:08:07  ClareS says "it is one of our hardest sections -- certainly the most mathematical"
16:08:56  CharafB says "Yes, it's seemes to be based on models extrapolating from little practical data"
16:09:08  SpyrosS says "Interesting. I felt at home with the maths, because of my physics background !"
16:09:27  ClareS says (to CharafB) "what do you mean exactly?"
16:10:49  ClareS says "the test of a molecular model is how well it can predict or reproduce a real structure"
16:11:08  CharafB says "I mean that the mathematical models to predict forces might be improved with time as data on 3D becomes greater, am I wrong?"
16:11:23  ClareS says "yes, of course"
16:11:56  ClareS says "but they haven't changed *very* much since structures were counted in hundreds rather than tens of thousands"
16:14:56  RamananS connects.
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16:15:11  ClareS says (to RamananS) "Hi"
16:15:24  RamananS says "sorry I am late"
16:15:27  CharafB says "Hi"
16:15:38  ClareS says (to RamananS) "we are discussing the basis for mathematical modelling..."
16:15:38  RamananS says "hello"
16:15:48  SpyrosS says "Hi"
16:15:53  ClareS says (to RamananS) "don't worry about it!"
16:17:07  ClareS says "how are you finding this section?"
16:17:44  RamananS says "I did not get a chance to go through it all yet"
16:17:58  RamananS says "but very interesting"
16:18:18  ClareS says "it is quite a long section.. I might try to put on an extra MUD towards the end of next week if people would like one"
16:18:36  RamananS says "yes please"
16:18:51  ClareS says "have any of you any experience with molecular modelling?"
16:19:14  RamananS says "not me"
16:19:17  CharafB says "I found that we were going to the deepest aspect of chemistry which is in fact physics!"
16:19:46  ClareS says "Biophysics, perhaps..."
16:20:12  SpyrosS says "Yes, that's what I am trying to do at present."
16:20:37  RamananS says "should we know Coulomb's law upwards by heart for the exams"
16:20:42  ClareS says "what software are you using?"
16:20:52  CharafB says "I have no experience with modeling at all"
16:21:05  ClareS says (to RamananS) "if you *can*.. but it's much more important to know the basic principles"
16:21:25  PaulW connects.
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16:21:45  ClareS says (to PaulW) "Hi"
16:22:05  CharafB says "Hi Paul"
16:22:06  SpyrosS says "I have just started to use GROMACS for molecular dynamics and DELPHI for electrostatic calculations"
16:22:10  PaulW says "hello"
16:22:14  ClareS says "we don't attempt to teach modelling itself on this course"
16:22:36  ClareS says "we do give you a glimpse of the theory behind it"
16:22:53  ClareS says (to SpyrosS) "these are good academic programs but not the easiest to use"
16:22:59  SpyrosS says (to PaulW) "Hi"
16:24:37  PaulW says "Hi spyrosS"
16:24:55  CharafB says "I think it is important to know what are the laws regulating proteins interaction, which are resumed in the force field formula Etot =...."
16:25:08  SpyrosS says (to ClareS) "Exactly!!"
16:25:33  ClareS says (to CharafB) "can you paste in the URL so we can find the correct page quickly?"
16:25:36  CharafB says "But I don't see myself programming that kind modelling softwares!"
16:26:14  ClareS says (to SpyrosS) "there are two types of modelling program -- excellent programs written by academics that are cheap and difficult to use..."
16:26:36  ClareS says "...and commercial giant packages that are user-friendly but cost the earth"
16:26:38  CharafB says "http://pps9900.cryst.bbk.ac.uk/ppscore/section7/forcefield.html"
16:26:53  ClareS says "and, of course, visualisation tools like rasmol"
16:27:09  ClareS says "which to be pedantic make up a third class"
16:27:27  KevinO connects.
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16:27:35  ClareS has found the equation...
16:29:38  AttilaR connects.
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16:29:52  ClareS says (to AttilaR) "Hi"
16:30:18  AttilaR says "Hello, sorry for being late!"
16:30:23  KevinO says "hi, sorry I'm late"
16:30:48  SpyrosS says "Hi"
16:30:59  CharafB says "Hi"
16:31:29  AttilaR says "What are we going to talk about this time?"
16:31:29  ClareS says "kevin & attila, we are looking at the force field equation: see http://pps9900.cryst.bbk.ac.uk/ppscore/section7/forcefield.html"
16:32:42  KevinO says (to ClareS) "got it"
16:32:57  ClareS says "a long time ago Charaf asked about the laws which regulated the interactions represented by the equation for Etot"
16:33:20  ClareS says (to CharafB) "can you expand further on what is puzzling you?"
16:33:51  CharafB says "I was wondering if we could Ee for errors accumulated in approximation of the partial forces"
16:34:15  CharafB says "sorry if we could ADD Ee"
16:34:40  AttilaR disconnects.
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16:35:03  ClareS says "it is very difficult to estimate such errors"
16:35:04  AttilaR connects.
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16:35:24  CharafB says "Models end up sometimes with puting to atoms exactly at the same place as mentionned somewhere in the ext about Van der Waals forces"
16:35:37  ClareS says "of course you always have to bear in mind that such an equation is an estimate"
16:35:56  VijayK connects.
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AttilaR      PPS          HTTP        52s      52s
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16:36:01  AttilaR says "Sorry, there hase been some problem with the connection."
16:36:12  CharafB says "This implies that some approximation errors are greater than expected"
16:36:26  ClareS says "if you wanted to be exactly accurate you would have to use quantum mechanics, and that is *impossible* for large molecules like proteins"
16:36:33  VijayK says "I have just got in sorry for being late"
16:37:05  ClareS says "it is quite surprising that molecular mechanics often gives such reasonable results"
16:37:22  ClareS says (to VijayK) "don't worry..."
16:39:00  CharafB says "Oh yes, of course, I am absolutely astonished by what we can make already but it's seems like there is ground for improvement which is great!"
16:39:09  VijayK says "Iam not familiar with this - molecular mechanics"
16:39:14  ClareS says "there is certainly ground for improvement..."
16:39:47  ClareS says (to VijayK) "molecular mechanics is the term used for modelling molecules using classical (not quantum) mechanics"
16:40:21  ClareS says "i.e. with "balls" and "sticks", bond lengths and angles rather than molecular orbitals"
16:40:30  VijayK says "Eaxmples of classical mechanics used commonly"
16:40:58  ClareS says "all the equations given in these section are classical mechanics equations"
16:41:27  VijayK says "Shall we be dealing with quantum mechanics in this course?"
16:41:27  CharafB says "No electron spin, then! ;)"
16:42:00  RamananS says "are 'optimum bond lengths' and  equilibrium bond lengths as in the bond sterching analysis the same?"
16:42:17  CharafB says "I have a simple query on page:"
16:42:21  CharafB says "http://pps9900.cryst.bbk.ac.uk/ppscore/section7/helix3.html"
16:42:32  ClareS says "no electron spin -- and no quantum mechanics in this course"
16:42:50  AttilaR says "I think sometimes it is very good to make understand things with these classical terms and equations, because they are more easily understood by me."
16:42:57  ClareS says "and yes, optimum bond lengths & equilibrium bond lengths are the same"
16:43:11  CharafB says "How is caculated the dipole moment?"
16:43:51  ClareS says "equilibrium bond length is in some ways a moer accurate term because it implies that bonds are not actually fixed rods"
16:45:17  ClareS says "I am not exactly sure how the dipole moment is calculated"
16:46:11  CharafB says "Would you know what is the unit... D doesn't ring a bell to me..."
16:46:45  ClareS says "it's based on the separation of partial charges on atoms but I don't know the maths"
16:46:57  ClareS says "charge divided by distance"
16:47:42  VijayK says "Regarding the section on Programs for Modelling - how much of it will be useful in this course?"
16:48:24  ClareS says "you don't *need* to use any of these programs to pass the course"
16:48:47  ClareS says "that section is included out of interest to give pointers to people who want to take the subject further"
16:48:58  VijayK says "Thanks it is good to know"
16:49:10  ClareS says "of course, some people do use modelling in their projects and that's OK but they don't have to"
16:49:21  RamananS says "in ....helix3.html the examples at the end , are they all hypothetical or known interactions ()[D"
16:50:07  ClareS says (to RamananS) "they are known interactions"
16:51:01  ClareS says "you can see this easiest if you look at the ligand - protein interactions in flavodoxin & lactate dehydrogenase"
16:51:46  ClareS says "e.g. in flavodoxin a negatively charged phosphate group in the ligand binds to..."
16:52:18  ClareS says "... the amino terminus of an alpha helix, which is slightly positively charged"
16:52:57  RamananS says "is it not half a unit charge not 'slight'?"
16:53:02  ClareS says "is that clear?"
16:53:18  ClareS says "less than a single electron..."
16:53:48  RamananS says "things are definitely clearer , I'll take a look again..."
16:54:13  VijayK says "In the section Hydrogen Bonds II, Iam a little puzzled by the terms CG-OD, CD-OE, CZ and NZ etc"
16:55:20  ClareS says (to VijayK) "they are shortened forms for particular side chain atoms and bonds"
16:55:32  KevinO says "on Dipole moments, the unit (D) is Debye and a reference to them is http://www.dartmouth.edu/artsci/chem/introchem/dipole.html"
16:55:47  ClareS says "e.g. CG-OD is a bond between a gamma-carbon atom and a delta-oxygen atom"
16:55:53  RamananS says "thanks Kev"
16:56:10  CharafB says (to KevinO) "Thanks!"
16:56:12  ClareS says (to KevinO) "Thanks -- I'd forgotten the name of the unit. Sorry..."
16:57:23  ClareS says "that URL gives a very clear description of the dipole moment defined as charge * distance"
16:58:24  VijayK says "Thanks again. Also thanks for the URL on dipole moment"""
16:59:01  ClareS is looking for an archived image of flavodoxin showing the interaction
17:00:12  CharafB says "Would anyone know a link to a quick refresher URL on thermodynamics, I studied enthalpy and entropy 10 years ago on 1st year at the vet school, it seems so far away!"
17:01:05  ClareS says "For flavodoxin: see http://www.biochem.ucl.ac.uk/bsm/pdbsum/2fdx/main.html"
17:01:18  ClareS says "that is an entry in the PDBsum database"
17:02:27  RamananS says "for thermodyn... try google.com with correct spelling and word 'y...."
17:02:27  ClareS says "if you follow the link to LIGPLOT you will see the negatively charged phosphate group binding to residues 7,8,9 and 12"
17:02:52  ClareS says "you will also see that those residues are at the N terminus of an alpha helix"
17:04:36  CharafB says (to RamananS) "Thanks very much, Ramanan!"
17:04:57  ClareS tried it and found a lot of books on the subject
17:06:25  ClareS says "Try Basic Chemical Thermodynamics: http://orac.sunderland.ac.uk/~hs0bcl/td1.htm"
17:08:22  ClareS says "that seems, at first glance, to be accessible and quite mathematical enough for this course"
17:08:51  CharafB says (to ClareS) "This looks great ... Thanks!"
17:10:32  ClareS says "nothing on entropy & the second law, tho' unfortunately"
17:11:14  ClareS says "I'd like to close the meeting quite soon: are there any more questions or points for discussion?"
17:11:48  KevinO says "not from me"
17:12:05  RamananS says "is ther e going to be a more MUD sessions on this section?"
17:12:30  AttilaR says "I think I have to go now."
17:13:35  VijayK says "Section 7 was great. but I have all the relevant sections on protein geometry etc to get the impact"
17:14:31  SpyrosS says "I have to go too, bye everyone"
17:14:38  KevinO says "'bye - lunch time!"
17:14:57  AttilaR disconnects.
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17:15:09  ClareS says (to VijayK) "there is more info on the names given to atoms in protein side chains at http://pps9900.cryst.bbk.ac.uk/ppscore/section3/jonc/conform.html"
17:15:10  KevinO disconnects.
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17:15:18  ClareS says "(in section 3)"
17:15:33  VijayK says "Thank you"
17:15:38  ClareS says "don't forget the session to-morrow at 23:00"
17:15:41  AttilaR connects.
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17:15:48  CharafB says "I would agree with Vijay, that's the basis for the rest"
17:16:32  SpyrosS disconnects.
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17:16:38  ClareS says "... and remember that British Summer Time starts next week. I will still give MUD times in GMT but the time in the UK will be different"
17:17:11  AttilaR says "Good bye everybody!"
17:17:28  AttilaR disconnects.
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17:17:36  CharafB says (to AttilaR) "Bye!"